Prevalence and Genetic Characterisation of Human Sapovirus from Children with Diarrhoea in the Rural Areas of Vhembe District, South Africa, 2017–2020

Abstract

Diarrhoeal disease is considered an important cause of morbidity and mortality in developing areas, and a large contributor to the burden of disease in children younger than five years of age. This study investigated the prevalence and genogroups of human sapovirus (SV) in children ≤5 years of age in rural communities of Vhembe district, South Africa. Between 2017 and 2020, a total of 284 stool samples were collected from children suffering with diarrhoea (n = 228) and from children without diarrhoea (n = 56). RNA extraction using Boom extraction method, and screening for SV using real-time PCR were done in the lab. Positive samples were subjected to conventional RT-PCR targeting the capsid fragment. Positive sample isolates were genotyped using Sanger sequencing. Overall SV were detected in 14.1% (40/284) of the stool samples (16.7% (38/228) of diarrhoeal and 3.6% (2/56) of non-diarrhoeal samples). Significant correlation between SV positive cases and water sources was noted. Genogroup-I was identified as the most prevalent strain comprising 81.3% (13/16), followed by SV-GII 12.5% (2/16) and SV-GIV 6.2% (1/16). This study provides valuable data on prevalence of SV amongst outpatients in rural and underdeveloped communities, and highlights the necessity for further monitoring of SV circulating strains as potential emerging strains.

A Descriptive Cross-Sectional Assessment of Caregivers’ Knowledge and Practices Regarding the Prevention and Management of Diarrhea among Children under the Age of Five in Thulamela B Clinics, South Africa

“…The discrepancies in results might be as a result of the setting as reported by [19] whose report in the rural and urban settings presented contradictory results in relation to germ infection as a cause of diarrhea. In corroboration with other studies [4,17,18,20], caregivers (69.3%) cited their understanding and some of the signs associated with diarrhea to be, passing of unformed or watery stool more than three times a day, presence of blood in the stool, abdominal pain as well as nausea/vomiting.…”

“…A major public health concern with regards to caregiver practices with drinking water are the reports of positive cases of sapovirus as well as a high distribution of Enterococcus faecalis and Eschericia. coli as fecal coliform bacteria in all the selected drinking water samples (municipal taps and boreholes, rivers and springs) collected at the point-of-use in study settings located in Vhembe District across all seasons [ 4 , 22 ].…”

“…Diarrheal infection may present in different ways depending on the causative pathogen. Diarrhea can be asymptomatic or mild accompanied by episodes of headaches, fever, acute abdominal pain, frequent nausea and vomiting, presence blood in stool or even death [ 2 , 4 , 5 ]. Diarrheal pathogens are commonly transmitted from one person to the other through the fecal-oral route, contaminated water or food, especially when there is poor environmental and personal sanitary hygiene [ 2 , 4 ].…”

“…Diarrhea can be asymptomatic or mild accompanied by episodes of headaches, fever, acute abdominal pain, frequent nausea and vomiting, presence blood in stool or even death [ 2 , 4 , 5 ]. Diarrheal pathogens are commonly transmitted from one person to the other through the fecal-oral route, contaminated water or food, especially when there is poor environmental and personal sanitary hygiene [ 2 , 4 ]. However, literature on studies carried out in different countries indicated that diarrhea risk factors among children aged 0–5 years vary in several dimensions such as environmental, economic or social dimensions [ 6 , 7 , 8 ].…”

Partial Analysis of the Capsid Protein (VP1) of Human Sapovirus Isolated from Children with Diarrhoea in Rural Communities of South Africa

“…Human SV has four well-known genogroups, namely, genogroups I, II, IV, and V. Although SV-GI is the most detected genogroup followed by SV-GII, these genogroups are commonly associated with acute gastroenteritis across age groups and often detected in infants [ 2 , 4 – 8 ]. There are few studies on the detection of human SV in South Africa which have been reported in different settings, that is, on rural outpatients [ 9 ], in a longitudinal study [ 10 ], on urban hospitalized children [ 11 , 12 ], and on all age groups [ 13 ].…”